<html>
<h3>Library Table</h3>
Top row of buttons:
<ul type="circle">
<li>Select one or more rows followed by "Genes" or "Trans", which will show the 
table of library counts for all gene(s) or transcript(s).
</ul>


<h4>Column descriptions</h4>
The database was built using a configuration file, which defines the "Lib Name" and conditions.
<br>
<table border=0>
<tr><td><i>Column name</i><td><i>Description</i>
<tr><td valign="top">LIBid<td>mySQL identifier, used internally
<tr><td valign="top">Lib Name<td>The library abbreviation.
<tr><td valign="top"><i>conditions</i><td>One or two columns with the condition names, e.g. Strain and Tissue
<tr><td valign="top">#Reps<td>Number of replicas that were sequenced for the library.
<tr><td valign="top">SNP Ref<td>Coverage for the reference allele.
<tr><td valign="top">SNP Alt<td>Coverage for the alternative allele.
<tr><td valign="top">SNP All<td>Total Coverage.

<tr><td valign="top">Read Ref<td>Number of reads assigned to reference; if loaded<sup>1,2</sup>
<tr><td valign="top">Read Alt<td>Number of reads assigned to alternative; if loaded<sup>1,2</sup>
<tr><td valign="top">Read All<td>Total number of reads; if loaded<sup>1,2</sup>
<br>Note that some genes or trans have no Ref/Alt difference  
<br>in which case the Ref/Alt counts will be zero. 
</table>
<p>
<sup>1</sup>These columns are not shown if the corresponding data is not in the database.
<br><sup>2</sup>Programs such as
eXpress (Roberts A, Pachter L (2013) Nat Methods 10: 71-73.) 
compute the estimated number of total
<br>reads for the reference and alternative by taking into account the variants. 

<h4>Manipulating the table</h4>
<ol>
<li>Columns can be moved around by selecting a column heading and moving it.
<li>Columns can be sorted by right click (descending); left click or second right click (ascending).
<li>To change the columns shown, select "Select" (next to the "Columns" label at the bottom of the window). 
<br>Selecting/deselecting a column immediately displays or removes it.
<li>When a new table is generated, it uses the last selected column settings. 
</ol>
</html>